GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Dinoroseobacter shibae DFL-12

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate 3607889 Dshi_1297 acyl-CoA dehydrogenase domain protein (RefSeq)

Query= BRENDA::Q96329
         (436 letters)



>FitnessBrowser__Dino:3607889
          Length = 387

 Score =  171 bits (433), Expect = 4e-47
 Identities = 114/376 (30%), Positives = 188/376 (50%), Gaps = 11/376 (2%)

Query: 55  LTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI-KGYGCPGL 113
           L  E +A+R+ V    ++ V P+  E      FP  + P++G +G+ G ++ + YG  G+
Sbjct: 10  LGEEVEALREMVHRWAQERVKPLAAETDRSNAFPNALWPEMGELGLLGITVDEAYGGAGM 69

Query: 114 SITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWA 173
              A+ +A  EI+R  AS       HS+L +  I L G++AQKEKYLP L     V   A
Sbjct: 70  GYLAHTVAVEEISRASASIGLSYGAHSNLCVNQIKLNGTDAQKEKYLPKLVSGAHVGALA 129

Query: 174 LTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFAR---NTTTNQINGF 230
           ++E   GSD  G+   A K    +++NG K WI N   AD L+++A+      +  I  F
Sbjct: 130 MSEAGAGSDVVGMKLRAEKRNDHYRLNGTKYWITNGPDADTLVVYAKTDPEAGSKGITAF 189

Query: 231 IVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRL----PGVNSFQDTSKVLAV 286
           +++K+  G   +   +K+G+R     +++ ++V VP E+ L     GV         L  
Sbjct: 190 LIEKEMAGFSTSPHFDKLGMRGSNTAELIFEDVEVPFENVLGEEGRGVAVLMSG---LDY 246

Query: 287 SRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWR 346
            RV+++   IGI  G  D    Y+ ER+QFG P+  FQL Q K+  M   + +     + 
Sbjct: 247 ERVVLSGVNIGIMAGCLDEVMPYMTERRQFGEPIGNFQLMQGKIADMYTAMNSARAYAYE 306

Query: 347 LCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYT 406
           + K  + G++T   A+    + S +  + A    + +GG G L D  VA+ F D + +  
Sbjct: 307 VAKACDRGEVTRQDAAACVLYASEEGMKVAHQAVQAMGGAGFLNDSPVARMFRDAKLMEI 366

Query: 407 YEGTYDINTLVTGREV 422
             GT +I  ++ GRE+
Sbjct: 367 GAGTSEIRRMLVGREL 382


Lambda     K      H
   0.319    0.133    0.399 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 347
Number of extensions: 21
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 436
Length of database: 387
Length adjustment: 31
Effective length of query: 405
Effective length of database: 356
Effective search space:   144180
Effective search space used:   144180
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory